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James Sacco
Laboratory for Genomics Research, University of California, San Francisco, San Francisco, CA 94158, USA
Self-motivated computational biologist with seven years of both academic and industry experience in genetic disease, functional genomics, and biomedical software development.
An analytical thinker and quick learner, with broad experience in AI/ML, gene regulatory network inference, and multi-omic single cell data analysis. Published manuscript on association of curated genotype, phenotype, and rare variant data to sub-type genetic disorders. Advocate for diversity and inclusion in STEM.
Selected Experience
Bioinformatics Programmer III
Laboratory for Genomics Research, University of California, San Francisco
San Francisco, CA
Present - 2022
● Led investigation of computational rules for CRISPR interference (CRISPRi) guide RNA design optimization, using Python machine learning modules.
● Improved whole-genome targeting of promoter regions in a genome-wide CRISPRi dual-guide library in K562 cancer cell lines.
● Identified over 100 putative therapeutic targets, as computational lead on a CRISPRi screen focused on cellular dysfunction in Niemann-Pick Type C Disease.
● Integrated single-cell epigenetic and transcriptomic data to computationally reconstruct gene regulatory networks for seventy-six transcription factors in iPSC-derived cells.
● Mentored two junior programmers on the computational biology team.
● Co-authored a manuscript officially intended for publication, on in-house experimental findings.
Bioinformatics Scientist
ASC Therapeutics
Milpitas, CA
2022 - 2021
● Quantifed and characterized CRISPR gene modifications in a sickle-cell disease model, with both in-house and open-source tools for genomic data analysis.
● Queried, retrieved, and integrated data from public genomics databases, to enhance on-target gene editing with sequence alignment protocols.
● Examined concordance and sensitivity of five computational CRISPR off-target error detection methods.
● Streamlined high-performance analyses for bench scientists via custom data pipelines and user interfaces, enabling round-the-clock analyses.
Biomarker Data Analyst II
Genentech (Contract)
South San Francisco, CA
2020 - 2019
● Established department-first machine learning pipeline to study effects of biomarker operations on quality of cancer immunotherapy assays.
PROGRAMMING SKILLS
Python ★★★★★
R ★★★★☆
Linux ★★★★☆
Git ★★★★★
Markdown★★★★★
C++ ★★★☆☆
MATLAB ★★★☆☆
● Upgraded data operations for six data streams, including flow cytometry, biomarker operations, and oncology data warehouses.
● Monitored and solved sample data quality issues for two cancer immunotherapy trial arms.
Data Curator
Genentech (Contract)
South San Francisco, CA
2019 - 2018
● Collaborated with AI engineers to create an ETL pipeline for multi-modal survival prediction and patient stratification, by using Python ML and R to integrate gene panel and RNA-Seq data.
● Designed ETL data pipeline for integration of real-world EHRs into deep learning module, using Python, SQL, and Apache Spark.
● Organized and managed close coordination of Artificial Intelligence, data management, and DevOps functions, to bring clinical machine learning from prototype to production.
● Provided AI and genomic analytic insights in collaboration with Roche-wide data curators and integrators network, to establish F.A.I.R. data management strategies for legacy, current, and next-generation datasets
● Tested data querying capabilities of newly-acquired AWS-based tech stack.
● Scoped design of in-house proteomics assay data ingestion and storage
Data Curator, Bioinformatics Analyst
BioMarin Pharmaceutical (Contract)
San Rafael, CA
2018 - 2017
● Established an integrated genetic and curated literature workflow to predict incidence and prevalence rates of over sixty rare, genetic disorders, with R statistical and data visualization packages and MATLAB.
● Upgraded and tested RNA-Seq data pipeline (STAR2, SAMtools, Bioconductor) to discern disease contribution of rare variants to neural disease.
● Spearheaded development of three relational databases derived from Hail population genomics platform, in collaboration with software engineer.
● Co-authored manuscript submitted to peer-reviewed publication, on prediction of disease severity in metachromatic leukodystrophy.
● Developed allele-specific association models and GWAS analysis software for two later published manuscripts.
I have participated in bioinformatics and software workshops and Meetup.com groups, in both Seattle, WA and San Francisco, CA, including:
SF/Bay AI Developers Group
San Jose Data Science and AI/ML Meetup
Hacker Dojo
Seattle Sequencing
LANGUAGES
English: Native Proficiency
Spanish: Native Proficiency
Dutch: Intermediate Proficiency
Research Associate
Pearse Lab: The Miami Project to Cure Paralysis, The Miller School of Medicine, University of Miami
Miami, FL
2017 - 2016
● Mentored research associates in developing bioinformatic skills, specifically in multiple sequence alignment and standard molecular biological protocols (restriction enzyme digestion, gel electrophoresis, spectrophotometry).
● Identified over forty putative conserved vertebrate phosphodiesterase proteins, by using multiple sequence alignment and genomic evidence.
Education
Rowan University, Graduate School of Biomedical Sciences
Master of Biomedical Science (Distinction)
Stratford, NJ
N/A
“Mechanisms of synaptic signaling dysfunction in hippocampal long-term potentiation”
Related coursework:
● Biochemistry
● Molecular Biology
● Cell Biology
● Mechanisms of Disease
● Pharmacology
Florida International University, The Honors College
BSc, Biological Sciences
Miami, FL
Professional Development
Publications
Predicting disease severity in metachromatic leukodystrophy using protein activity and a patient phenotype matrix.
Genome Biology. 2023 Jul 24:172.
N/A
2023
Trinidad M., Hong X., Froelich S., Daiker J., Sacco J., Phuc Nguyen H., Campagna M., Suhr D., Suhr T., LeBowitz J.H., Gelb M.H., Clark W.T.
Regulating Axonal Responses to Injury: The Intersection between Signaling Pathways Involved in Axon Myelination and The Inhibition of Axon Regeneration.
Frontiers in Molecular Neuroscience. 2016 Jun 8;9:33.
N/A
2016
Rao S.N., Pearse D.D. Manuscript Editor
Conferences
Single Cell Analyses
Cold Spring Harbor Laboratory Single Cell Analyses Meeting.
Cold Spring Harbor, New York
2023
Prediction of disease severity in metachromatic leukodystrophy using measures of protein activity and a novel phenotype matrix.
American Society of Human Genetics Virtual Meeting. [Poster]
Online
2020
Trinidad M., Hong X., Sacco J., Nguyen H.P., Clark W.T., Froelich S., LeBowitz J.H., Gelb M.H.
Association of HGMD and gnomAD variants of unknown significance with prediction of disease incidence and prevalence.
BioMarin Internal Research and Development Asilomar Conference. [Poster]
Pacific Grove, CA
2018
Sacco J., Clark W.T., Yu K., Wu K., LeBowitz J.H.
Research Projects
Characterization of glycan substrates accumulating in GM1 gangliosidosis
Molecular Genetics and Metabolism Reports. 2019. 21, p.100524.
N/A
2019
Lawrence R., et al.
Phosphodiesterase Inhibitors as a Therapeutic Approach to Neuroprotection and Repair
International Journal of Molecular Sciences. 2017. 18(4): 696.
N/A
2017
HOBBIES
Stonewall Sports kickball. San Francisco, CA. 2023 – Present.
Ultimate frisbee player. San Francisco, CA. 2018 – Present.
Rugby at Seattle Quake RFC. Seattle, WA. 2016 – 2017.
Knott E.P., et al.
Oral Communications
Data Visualization of RNA-Seq Differential Expression Analysis with DESeq2
Doudna Lab: Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California, Berkeley
Berkeley, CA
2022
Topics: Introduction to RNA-Seq, Standard Workflows with DESeq2, Reference-Based Assembly, Exploratory Data Analysis, Statistical Analysis, Data Visualization, Gene Set Enrichment, Variant Annotation
● Presented publication-quality RNA-Seq data summaries and representations to post-doctoral associates
Changes in chromatin accessibility are not concordant with transcriptional changes for single-factor perturbations
Laboratory for Genomics Research & Department Biochemistry & Biophysics, University of California, San Francisco
San Francisco, CA
2022
● Presented now-published preprint in contrast with established research at internal Journal Club to inform future experimental design in epigenetic editing.
Teaching
Peer-Led Team Learning
Florida International University
Miami, FL
2009
General Biology II facilitator for two concurrent PLTL courses
Disclaimer
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Last update: 2023-11-14.The most recent version of this resume is available here.